BioNetVisA 2015 workshop
From biological network
reconstruction to data visualization and analysis in molecular biology and
medicine
25 November 2015
Yong Loo Lin School of
Medicine
National University of
Singapore (NUS)
Singapore
Downloads
Program and abstracts booklet 2015 Presentation slides 2015
BioNetVisA
workshop brings together different actors of network biology from database
providers, networks creators, computational biologists, biotech companies
involved in data analysis and modeling to experimental biologists, clinicians that
use systems biology approaches. The participants are exposed to the different
paradigms of network biology and the latest achievements in the field.
Motivation
The goal of BioNetVisA workshop is to build a discussion around various
approaches for biological knowledge formalisation, data integration and
analysis; compatibility between different methods and biological networks resources
available the field; applicability for concrete research and clinical projects
depending on scientific question and type of high-throughput data.
The BioNetVisA workshop aims at identifying bottlenecks and proposing
short- and long-term objectives for the community as discussing questions about
accessibility of available tools for wide range of user in every-day standalone
application in biological and clinical labs. In addition, the possibilities for
collective efforts by academic researchers, clinicians, biotech companies and
future development directions in the field will be discussed during the round
table panel.
Topics
Graphical representation of biological knowledge
Molecular interaction and pathway databases
Comprehensive signalling networks
Networks annotation and curation
High-throughput data visualisation, analysis
and interpretation in the context of networks
Network modelling
Basic research and clinical application of network
biology
Scope
Development, curation and
maintenance of biological network databases
Data models from interaction to pathway and
network, available tools for the integration of new discoveries into existing
signalling diagrams. Discussion of curation models from map manager-oriented to
community-based update using web-tools and forums.
Cell signalling knowledge
representation paradigms
From interaction to single pathways
representation to comprehensive signalling networks: discussion of modes of
biological processes representation; granularity, coverage, sources of
information, annotation modes, cross-citations between different signalling
networks resources, etc. Standard data formats, graphical representation
standards.
Visualization of data through
networks
Paradigms of visualization of different types
of high-throughput data on a network map. Data integration with a map. Methods
compatibility with different paradigms of signalling networks reconstruction in
various databases and resources.
Analytical tools for network
biology
Tools for network analysis and manipulation,
network modeling, network-based statistics. Studying network activation and
inhibition, feedbacks and compensations, synthetic interactions, clinical treatment
response and resistance.
Registration
The registration has to be performed via ICSB site
Program
Session 1
Development of biological network databases and platforms
9.00-9.30
Garuda Platform and Its Applications in Biomedical
Research
Yukiko Matsuoka (Systems Biology Institute, Tokyo, Japan)
9.30-10.00
PhysioDesigner: A versatile
platform for multilevel modeling of physiological systems network
Yoshiyuki Asai (The Okinawa Institute of Science and
Technology, Okinawa, Japan) Abstract Slides
10.00-10.30
Studying
cancer biology big data with Google Maps: NaviCell Web Service and Atlas of
Cancer Signaling Network
Andrei
Zinovyev (Institut Curie, Paris,
France)
10.30-10.45 Break
10.45-11.05
SIGNOR:
a database of causal relationships between biological entities
Livia Perfetto (University of Rome Tor Vergata, Rome, Italy)
11.05-11.55
Keynote lecture
Molecular networks as determinants of response
and outcome
Lodewyk
Wessels (Netherlands Cancer Institute, Amsterdam, Netherlands)
12.00-13.30 Lunch
Session 2
Data visualisation and analysis in the context of biological
networks in research and medicine
13.30-13.50
NetLand: A comprehensive tool for
simulation and visualization of transcriptional network kinetics
Jie Zheng (Nanyang
Technological University, Singapore)
13.50-14.10
Significant prognostic gene and interconnection
network enrichment (SPGINE) analysis
stratifies breast cancers into three reproducible subclasses determined by
novel genetic grading signatures
Vladimir Kuznetsov (Bioinformatics Institute, Singapore)
14.10-14.30
Prediction of
sensitivity to genotoxic drug by modeling cancer cell lines and
patient omics data in
the context of comprehensive DNA repair signaling network
Inna
Kuperstein (Institut
Curie, Paris, France)
14.30-14.50
Communities
and Disease Comorbidities from Multiplex Biological Networks
Anaïs Baudot (CNRS-AMU, Marseilles,
France)
14.50-15.00 Break
Session3
Modelling of biological networks
15.00-15.30
Predictive logical modelling of cell fate decision networks
Denis Thieffry (IBENS, Ecole Normale Supérieure, Paris,
France)
15.30-15.50
Computing Life:
Blue-print modelling and domino approach in design principle studies of
Reactive Oxygen Species management
Alexey Kolodkin (University of Luxembourg, Luxembourg)
15.50-16.10
Multiscale model to
recapitulate breast cancer invasion phenotypes
Arnau Montagud (Institut Curie, Paris, France)
16.10-17.00
Keynote lecture
Data-based
modeling of signal-transcription network for cell fate control
Mariko
Okada (RIKEN Center for Integrative Medical Sciences Yokohama, Japan)
17.00-17.10
Break
17.10-17.50
Round table discussion
17.50-18.00
Conclusions
Venue
Block
MD7, Seminar Room M9
Yong
Loo Lin School of Medicine
National
University of Singapore (NUS)
The
nearest train station: Kent Ridge Station on the Circle line
Directions: http://www.med.nus.edu.sg/bch/contact.htm
Organising Committee
Inna
Kuperstein
(Institut Curie, France)
Emmanuel Barillot (Institut Curie, France)
Andrei Zinovyev (Institut Curie, France)
Hiroaki
Kitano
(Okinawa Institute of Science and Technology Graduate University, RIKEN Center
for Integrative Medical Sciences, Japan)
Nicolas Le Novère (Babraham Institute, UK)
Robin
Haw
(Ontario Institute for Cancer Research, Canada)
Alfonso
Valencia (Spanish National Bioinformatics
Institute, Madrid, Stain)
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